Noncoding RNAs (ncRNAs) are now believed to be transcribed pervasively in the genome, and large numbers of ncRNAs have been identified. However, disproportionally, still very little is known about their functional roles. Many of the known ncRNA functions were inferred by perturbation experiments, which lack the details of what specific target an ncRNA interact with. Technologies like CLIP/RIP-Seq and ChiRP-Seq have provided tremendous insights of what the protein factors and chromatin loci for some ncRNAs to interact with. However, current methods are limited to examine ncRNA or interacting target one at a time. Thus it is desirable to have an unbiased genome-wide strategy to identify the functional targets for all ncRNAs.